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万見- EMDB-12847: State C of the human mitoribosomal large subunit assembly intermediate -
+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-12847 | ||||||||||||
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タイトル | State C of the human mitoribosomal large subunit assembly intermediate | ||||||||||||
マップデータ | state C | ||||||||||||
試料 |
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キーワード | mitoribosome / assembly intermediate / large subunit / LSU / mt-LSU / RIBOSOME | ||||||||||||
機能・相同性 | 機能・相同性情報 regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / tRNA (cytidine-5-)-methyltransferase activity / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / Complex I biogenesis / protein lipoylation / negative regulation of ribosome biogenesis ...regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / tRNA (cytidine-5-)-methyltransferase activity / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / Complex I biogenesis / protein lipoylation / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / rRNA import into mitochondrion / rRNA methyltransferase activity / mitochondrial [2Fe-2S] assembly complex / Respiratory electron transport / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / positive regulation of mitochondrial translation / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / iron-sulfur cluster assembly complex / protein targeting to mitochondrion / mitochondrial large ribosomal subunit binding / mitochondrial fission / camera-type eye development / mitochondrial large ribosomal subunit / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エンドリボヌクレアーゼ / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / rRNA methylation / [2Fe-2S] cluster assembly / aminoacyl-tRNA hydrolase activity / respiratory chain complex I / mitochondrial ribosome / iron-sulfur cluster assembly / mitochondrial translation / ribosomal large subunit binding / proton motive force-driven mitochondrial ATP synthesis / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / acyl binding / anatomical structure morphogenesis / acyl carrier activity / RNA processing / Mitochondrial protein degradation / aerobic respiration / rescue of stalled ribosome / ribosomal large subunit biogenesis / 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの / cellular response to leukemia inhibitory factor / methyltransferase activity / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / rRNA processing / double-stranded RNA binding / small ribosomal subunit rRNA binding / cell junction / ribosome biogenesis / heart development / large ribosomal subunit rRNA binding / double-stranded DNA binding / 5S rRNA binding / endonuclease activity / mitochondrial inner membrane / negative regulation of translation / nuclear body / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / ribonucleoprotein complex / translation / protein domain specific binding / GTPase activity / mRNA binding / nucleotide binding / calcium ion binding / synapse / GTP binding / regulation of DNA-templated transcription / nucleolus / apoptotic process / magnesium ion binding / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.1 Å | ||||||||||||
データ登録者 | Lenarcic T / Jaskolowski M / Leibundgut M / Scaiola A / Schoenhut T / Saurer M / Lee RG / Rackham O / Filipovska A / Ban N | ||||||||||||
資金援助 | スイス, 3件
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引用 | ジャーナル: Nat Commun / 年: 2021 タイトル: Stepwise maturation of the peptidyl transferase region of human mitoribosomes. 著者: Tea Lenarčič / Mateusz Jaskolowski / Marc Leibundgut / Alain Scaiola / Tanja Schönhut / Martin Saurer / Richard G Lee / Oliver Rackham / Aleksandra Filipovska / Nenad Ban / 要旨: Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have diverged considerably from the ancestral ...Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have diverged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs. The structural basis of the mammalian mitochondrial ribosome assembly is currently not well understood. Here we present eight distinct assembly intermediates of the human large mitoribosomal subunit involving seven assembly factors. We discover that the NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA in a conformation that exposes the functionally important regions of rRNA for modification by the MRM2 methyltransferase and quality control interactions with the conserved mitochondrial GTPase MTG2 that contacts the sarcin-ricin loop and the immature active site. The successive action of these factors leads to the formation of the peptidyl transferase active site of the mitoribosome and the folding of the surrounding rRNA regions responsible for interactions with tRNAs and the small ribosomal subunit. | ||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_12847.map.gz | 324.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12847-v30.xml emd-12847.xml | 76.3 KB 76.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_12847.png | 109 KB | ||
Filedesc metadata | emd-12847.cif.gz | 16.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12847 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12847 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_12847_validation.pdf.gz | 606.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_12847_full_validation.pdf.gz | 605.8 KB | 表示 | |
XML形式データ | emd_12847_validation.xml.gz | 7.7 KB | 表示 | |
CIF形式データ | emd_12847_validation.cif.gz | 8.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12847 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12847 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_12847.map.gz / 形式: CCP4 / 大きさ: 343 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | state C | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
+全体 : State C of the human mitoribosomal large subunit assembly intermediate
+超分子 #1: State C of the human mitoribosomal large subunit assembly intermediate
+分子 #1: Mitochondrial ribosome-associated GTPase 2
+分子 #2: Mitochondrial assembly of ribosomal large subunit protein 1
+分子 #3: MIEF1 upstream open reading frame protein
+分子 #4: Acyl carrier protein, mitochondrial
+分子 #5: 5-methylcytosine rRNA methyltransferase NSUN4
+分子 #6: Transcription termination factor 4, mitochondrial
+分子 #7: 39S ribosomal protein L32, mitochondrial
+分子 #8: 39S ribosomal protein L33, mitochondrial
+分子 #9: 39S ribosomal protein L34, mitochondrial
+分子 #10: 39S ribosomal protein L35, mitochondrial
+分子 #11: 39S ribosomal protein L36, mitochondrial
+分子 #12: 39S ribosomal protein L37, mitochondrial
+分子 #13: 39S ribosomal protein L38, mitochondrial
+分子 #14: 39S ribosomal protein L39, mitochondrial
+分子 #15: 39S ribosomal protein L40, mitochondrial
+分子 #16: 39S ribosomal protein L41, mitochondrial
+分子 #19: 39S ribosomal protein L2, mitochondrial
+分子 #20: 39S ribosomal protein L3, mitochondrial
+分子 #21: 39S ribosomal protein L4, mitochondrial
+分子 #22: 39S ribosomal protein L9, mitochondrial
+分子 #23: 39S ribosomal protein L10, mitochondrial
+分子 #24: 39S ribosomal protein L11, mitochondrial
+分子 #25: 39S ribosomal protein L13, mitochondrial
+分子 #26: 39S ribosomal protein L14, mitochondrial
+分子 #27: 39S ribosomal protein L15, mitochondrial
+分子 #28: 39S ribosomal protein L16, mitochondrial
+分子 #29: 39S ribosomal protein L17, mitochondrial
+分子 #30: 39S ribosomal protein L18, mitochondrial
+分子 #31: 39S ribosomal protein L19, mitochondrial
+分子 #32: 39S ribosomal protein L20, mitochondrial
+分子 #33: 39S ribosomal protein L21, mitochondrial
+分子 #34: 39S ribosomal protein L22, mitochondrial
+分子 #35: 39S ribosomal protein L23, mitochondrial
+分子 #36: 39S ribosomal protein L24, mitochondrial
+分子 #37: 39S ribosomal protein L27, mitochondrial
+分子 #38: 39S ribosomal protein L28, mitochondrial
+分子 #39: 39S ribosomal protein L47, mitochondrial
+分子 #40: 39S ribosomal protein L30, mitochondrial
+分子 #41: 39S ribosomal protein L42, mitochondrial
+分子 #42: 39S ribosomal protein L43, mitochondrial
+分子 #43: 39S ribosomal protein L44, mitochondrial
+分子 #44: 39S ribosomal protein L45, mitochondrial
+分子 #45: 39S ribosomal protein L46, mitochondrial
+分子 #46: 39S ribosomal protein L48, mitochondrial
+分子 #47: 39S ribosomal protein L49, mitochondrial
+分子 #48: 39S ribosomal protein L50, mitochondrial
+分子 #49: 39S ribosomal protein L51, mitochondrial
+分子 #50: 39S ribosomal protein L52, mitochondrial
+分子 #51: 39S ribosomal protein L53, mitochondrial
+分子 #52: 39S ribosomal protein L54, mitochondrial
+分子 #53: 39S ribosomal protein L55, mitochondrial
+分子 #54: Ribosomal protein 63, mitochondrial
+分子 #55: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+分子 #56: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+分子 #57: 39S ribosomal protein S18a, mitochondrial
+分子 #58: 39S ribosomal protein S30, mitochondrial
+分子 #17: 16S mitochondrial rRNA
+分子 #18: mitochondrial tRNAVal
+分子 #59: GUANOSINE-5'-DIPHOSPHATE
+分子 #60: MAGNESIUM ION
+分子 #61: S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYL...
+分子 #62: S-ADENOSYLMETHIONINE
+分子 #63: ZINC ION
+分子 #64: POTASSIUM ION
+分子 #65: FE2/S2 (INORGANIC) CLUSTER
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.6 構成要素:
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グリッド | モデル: Quantifoil R2/2 / 材質: COPPER / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS | ||||||||||
凍結 | 凍結剤: ETHANE-PROPANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV 詳細: 4 uL of the sample was blotted for 2-6 sec before plunging. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 60.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 100.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: OTHER |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: cryoSPARC (ver. 3.1) / 使用した粒子像数: 62552 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: cryoSPARC (ver. 3.1) |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: cryoSPARC (ver. 3.1) |